From 03cc7c74447cea87dee0897c3c881e6f3bf0e3b6 Mon Sep 17 00:00:00 2001
From: Christoph Lehmann <christoph.lehmann@ufz.de>
Date: Thu, 29 Aug 2024 07:53:07 +0200
Subject: [PATCH] [T/TRM] Added 0d confined compression test
---
.../confined_compression.prj | 457 ++++++++++++++++++
...confined_compression_ts_120_t_1.500000.vtu | 101 ++++
...confined_compression_ts_160_t_2.000000.vtu | 101 ++++
...confined_compression_ts_200_t_2.500000.vtu | 101 ++++
...confined_compression_ts_240_t_3.000000.vtu | 101 ++++
...confined_compression_ts_280_t_3.500000.vtu | 101 ++++
...confined_compression_ts_320_t_4.000000.vtu | 101 ++++
...confined_compression_ts_360_t_4.500000.vtu | 101 ++++
...confined_compression_ts_400_t_5.000000.vtu | 101 ++++
.../confined_compression_ts_40_t_0.500000.vtu | 101 ++++
...confined_compression_ts_440_t_5.500000.vtu | 101 ++++
...confined_compression_ts_480_t_6.000000.vtu | 101 ++++
.../confined_compression_ts_80_t_1.000000.vtu | 101 ++++
.../generate-reference-solution.py | 120 +++++
.../0d_confined_compression/meshes | 1 +
.../0d_confined_compression/ogs_and_mfront.py | 376 ++++++++++++++
16 files changed, 2166 insertions(+)
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression.prj
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_120_t_1.500000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_160_t_2.000000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_200_t_2.500000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_240_t_3.000000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_280_t_3.500000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_320_t_4.000000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_360_t_4.500000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_400_t_5.000000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_40_t_0.500000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_440_t_5.500000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_480_t_6.000000.vtu
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_80_t_1.000000.vtu
create mode 100755 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/generate-reference-solution.py
create mode 120000 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/meshes
create mode 100644 Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/ogs_and_mfront.py
diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression.prj b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression.prj
new file mode 100644
index 00000000000..17fcdfcb370
--- /dev/null
+++ b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression.prj
@@ -0,0 +1,457 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<OpenGeoSysProject>
+ <meshes>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8.vtu</mesh>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8_whole_surface.vtu</mesh>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8_x0.vtu</mesh>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8_y0.vtu</mesh>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8_z0.vtu</mesh>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8_x1.vtu</mesh>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8_y1.vtu</mesh>
+ <mesh axially_symmetric="false">meshes/cube_1e0_1x1x1_hex8_z1.vtu</mesh>
+ </meshes>
+ <processes>
+ <process>
+ <name>TRM</name>
+ <type>THERMO_RICHARDS_MECHANICS</type>
+ <subtype>StressSaturation_StrainPressureTemperature</subtype>
+ <integration_order>3</integration_order>
+ <constitutive_relation>
+ <type>MFront</type>
+ <behaviour>BentoniteBehaviour</behaviour>
+ <library path_is_relative_to_prj_file="false">libOgsMFrontBehaviourBentoniteGeneralModForCTestsOnly</library>
+ <initial_values>
+ <state_variable name="e" parameter="e0"/>
+ <state_variable name="em" parameter="em0"/>
+ <state_variable name="eM" parameter="eM0"/>
+ <state_variable name="SrM" parameter="SrM0"/>
+ <state_variable name="a_scan" parameter="a_scan0"/>
+ <state_variable name="re" parameter="re0"/>
+ </initial_values>
+ </constitutive_relation>
+ <process_variables>
+ <temperature>temperature</temperature>
+ <pressure>pressure</pressure>
+ <displacement>displacement</displacement>
+ </process_variables>
+ <secondary_variables>
+ <secondary_variable internal_name="sigma_total" output_name="sigma_total"/>
+ <secondary_variable internal_name="epsilon" output_name="epsilon"/>
+ </secondary_variables>
+ <specific_body_force>0 0 0</specific_body_force>
+ <initial_stress type="total">initial_stress</initial_stress>
+ </process>
+ </processes>
+ <media>
+ <medium id="0">
+ <phases>
+ <phase>
+ <type>AqueousLiquid</type>
+ <properties>
+ <property>
+ <name>specific_heat_capacity</name>
+ <type>Constant</type>
+ <value>4280.0</value>
+ </property>
+ <property>
+ <name>thermal_conductivity</name>
+ <type>Constant</type>
+ <value>0.6</value>
+ </property>
+ <property>
+ <name>density</name>
+ <type>Constant</type>
+ <value>999.1</value>
+ </property>
+ <property>
+ <name>thermal_expansivity</name>
+ <type>Constant</type>
+ <value>1e-5</value>
+ </property>
+ <property>
+ <name>viscosity</name>
+ <type>Constant</type>
+ <value>1.e-3</value>
+ </property>
+ </properties>
+ </phase>
+ <phase>
+ <type>Solid</type>
+ <properties>
+ <property>
+ <name>density</name>
+ <type>Constant</type>
+ <value>2290</value>
+ </property>
+ <property>
+ <name>thermal_conductivity</name>
+ <type>Constant</type>
+ <value>1.838</value>
+ </property>
+ <property>
+ <name>specific_heat_capacity</name>
+ <type>Constant</type>
+ <value>917.654</value>
+ </property>
+ <property>
+ <name>thermal_expansivity</name>
+ <type>Constant</type>
+ <value>1e-5</value>
+ </property>
+ </properties>
+ </phase>
+ </phases>
+ <properties>
+ <property>
+ <name>saturation</name>
+ <type>Constant</type>
+ <value>0.345</value>
+ </property>
+ <property>
+ <name>relative_permeability</name>
+ <type>Constant</type>
+ <value>1</value>
+ </property>
+ <property>
+ <name>permeability</name>
+ <type>Constant</type>
+ <value>2e-20</value>
+ </property>
+ <property>
+ <name>porosity</name>
+ <type>Constant</type>
+ <value>0.16</value>
+ </property>
+ <property>
+ <name>bishops_effective_stress</name>
+ <type>BishopsPowerLaw</type>
+ <exponent>1.0</exponent>
+ </property>
+ <property>
+ <name>biot_coefficient</name>
+ <type>Constant</type>
+ <value>1.0</value>
+ </property>
+ <property>
+ <name>thermal_conductivity</name>
+ <type>EffectiveThermalConductivityPorosityMixing</type>
+ </property>
+ </properties>
+ </medium>
+ </media>
+ <time_loop>
+ <processes>
+ <process ref="TRM">
+ <nonlinear_solver>basic_newton</nonlinear_solver>
+ <convergence_criterion>
+ <type>PerComponentDeltaX</type>
+ <norm_type>INFINITY_N</norm_type>
+ <abstols>1e-9 1e-6 1e-9 1e-9 1e-9</abstols>
+ </convergence_criterion>
+ <time_discretization>
+ <type>BackwardEuler</type>
+ </time_discretization>
+ <time_stepping>
+ <type>FixedTimeStepping</type>
+ <t_initial>0</t_initial>
+ <t_end>6</t_end>
+ <timesteps>
+ <pair>
+ <repeat>1</repeat>
+ <delta_t>0.0125</delta_t>
+ </pair>
+ </timesteps>
+ </time_stepping>
+ </process>
+ </processes>
+ <output>
+ <type>VTK</type>
+ <prefix>confined_compression</prefix>
+ <timesteps>
+ <pair>
+ <repeat>1</repeat>
+ <each_steps>1</each_steps>
+ </pair>
+ </timesteps>
+ <variables>
+ </variables>
+ <suffix>_ts_{:timestep}_t_{:time}</suffix>
+ </output>
+ </time_loop>
+ <parameters>
+ <parameter>
+ <mesh>cube_1e0_1x1x1_hex8</mesh>
+ <name>initial_stress</name>
+ <type>Function</type>
+ <expression>-2e6</expression>
+ <expression>-2e6</expression>
+ <expression>-2e6</expression>
+ <expression>0</expression>
+ <expression>0</expression>
+ <expression>0</expression>
+ </parameter>
+ <parameter>
+ <name>e0</name>
+ <type>Constant</type>
+ <value>0.9</value>
+ </parameter>
+ <parameter>
+ <name>em0</name>
+ <type>Constant</type>
+ <value>0.0</value>
+ </parameter>
+ <parameter>
+ <name>eM0</name>
+ <type>Constant</type>
+ <value>0.0</value>
+ </parameter>
+ <parameter>
+ <name>SrM0</name>
+ <type>Constant</type>
+ <value>0.0</value>
+ </parameter>
+ <parameter>
+ <name>a_scan0</name>
+ <type>Constant</type>
+ <value>0.0</value>
+ </parameter>
+ <parameter>
+ <name>re0</name>
+ <type>Constant</type>
+ <value>0.0</value>
+ </parameter>
+ <parameter>
+ <name>displacement0</name>
+ <type>Constant</type>
+ <values>0 0 0</values>
+ </parameter>
+ <parameter>
+ <name>pressure_ic</name>
+ <type>Constant</type>
+ <values>-110e6</values>
+ </parameter>
+ <parameter>
+ <name>temperature_ic</name>
+ <type>Constant</type>
+ <value>273.15</value>
+ </parameter>
+ <parameter>
+ <name>zero</name>
+ <type>Constant</type>
+ <value>0</value>
+ </parameter>
+ <parameter>
+ <name>one</name>
+ <type>Constant</type>
+ <value>1</value>
+ </parameter>
+ <parameter>
+ <name>pressure_bc</name>
+ <type>CurveScaled</type>
+ <curve>p_curve</curve>
+ <parameter>one</parameter>
+ </parameter>
+ <parameter>
+ <name>stress_xx</name>
+ <type>CurveScaled</type>
+ <curve>sigma_curve</curve>
+ <parameter>one</parameter>
+ </parameter>
+ </parameters>
+ <curves>
+ <curve>
+ <name>p_curve</name>
+ <coords>0.0 3.0</coords>
+ <values>-110e6 -110e6</values>
+ </curve>
+ <curve>
+ <name>sigma_curve</name>
+ <coords>0.0 6.0</coords>
+ <values>-2e6 -4e6</values>
+ </curve>
+ </curves>
+ <process_variables>
+ <process_variable>
+ <name>displacement</name>
+ <components>3</components>
+ <order>1</order>
+ <initial_condition>displacement0</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_x0</mesh>
+ <type>Dirichlet</type>
+ <component>0</component>
+ <parameter>zero</parameter>
+ </boundary_condition>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_y0</mesh>
+ <type>Dirichlet</type>
+ <component>1</component>
+ <parameter>zero</parameter>
+ </boundary_condition>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_z0</mesh>
+ <type>Dirichlet</type>
+ <component>2</component>
+ <parameter>zero</parameter>
+ </boundary_condition>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_x1</mesh>
+ <type>Neumann</type>
+ <component>0</component>
+ <parameter>stress_xx</parameter>
+ </boundary_condition>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_y1</mesh>
+ <type>Dirichlet</type>
+ <component>1</component>
+ <parameter>zero</parameter>
+ </boundary_condition>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_z1</mesh>
+ <type>Dirichlet</type>
+ <component>2</component>
+ <parameter>zero</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <process_variable>
+ <name>pressure</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>pressure_ic</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_whole_surface</mesh>
+ <type>Dirichlet</type>
+ <component>0</component>
+ <parameter>pressure_bc</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ <process_variable>
+ <name>temperature</name>
+ <components>1</components>
+ <order>1</order>
+ <initial_condition>temperature_ic</initial_condition>
+ <boundary_conditions>
+ <boundary_condition>
+ <mesh>cube_1e0_1x1x1_hex8_whole_surface</mesh>
+ <type>Dirichlet</type>
+ <component>0</component>
+ <parameter>temperature_ic</parameter>
+ </boundary_condition>
+ </boundary_conditions>
+ </process_variable>
+ </process_variables>
+ <nonlinear_solvers>
+ <nonlinear_solver>
+ <name>basic_newton</name>
+ <type>Newton</type>
+ <max_iter>50</max_iter>
+ <linear_solver>general_linear_solver</linear_solver>
+ </nonlinear_solver>
+ </nonlinear_solvers>
+ <linear_solvers>
+ <linear_solver>
+ <name>general_linear_solver</name>
+ <eigen>
+ <solver_type>SparseLU</solver_type>
+ <scaling>1</scaling>
+ </eigen>
+ <petsc>
+ <parameters>-ksp_type cg
+ -pc_type lu
+ -ksp_rtol 1.e-14 -ksp_atol 1.e-14
+ -ksp_max_it 4000
+ </parameters>
+ </petsc>
+ </linear_solver>
+ </linear_solvers>
+ <test_definition>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>epsilon_ip</field>
+ <absolute_tolerance>4e-09</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- inf --></relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_RungeKutta_InternalStateVariables[0]_ip</field>
+ <absolute_tolerance>0.0</absolute_tolerance>
+ <relative_tolerance>0.0</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_RungeKutta_InternalStateVariables[1]_ip</field>
+ <absolute_tolerance>0.0</absolute_tolerance>
+ <relative_tolerance>0.0</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_RungeKutta_InternalStateVariables[2]_ip</field>
+ <absolute_tolerance>0.0</absolute_tolerance>
+ <relative_tolerance>0.0</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_RungeKutta_InternalStateVariables[3]_ip</field>
+ <absolute_tolerance>0.0</absolute_tolerance>
+ <relative_tolerance>0.0</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_SrM_ip</field>
+ <absolute_tolerance>1.5e-10</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- 1.6e-08 --></relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_a_scan_ip</field>
+ <absolute_tolerance>0.0</absolute_tolerance>
+ <relative_tolerance>0.0</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_eM_ip</field>
+ <absolute_tolerance>5.3e-09</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- 1.2e-08 --></relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_e_ip</field>
+ <absolute_tolerance>6.8e-09</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- 8.1e-09 --></relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_em_ip</field>
+ <absolute_tolerance>1.2e-10</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- 4.3e-10 --></relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>material_state_variable_re_ip</field>
+ <absolute_tolerance>8.9e-09</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- 9.2e-09 --></relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>pressure</field>
+ <absolute_tolerance>0.0</absolute_tolerance>
+ <relative_tolerance>0.0</relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>saturation_ip</field>
+ <absolute_tolerance>2.6e-09</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- 7.9e-09 --></relative_tolerance>
+ </vtkdiff>
+ <vtkdiff>
+ <regex>confined_compression_ts_.*_t_.*[.]vtu</regex>
+ <field>sigma_total_ip</field>
+ <absolute_tolerance>0.16</absolute_tolerance>
+ <relative_tolerance>0.0 <!-- inf --></relative_tolerance>
+ </vtkdiff>
+ </test_definition>
+</OpenGeoSysProject>
diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_120_t_1.500000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_120_t_1.500000.vtu
new file mode 100644
index 00000000000..470fdd6020b
--- /dev/null
+++ b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_120_t_1.500000.vtu
@@ -0,0 +1,101 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+ <UnstructuredGrid>
+ <FieldData>
+ <DataArray type="Float64" Name="epsilon_ip" NumberOfComponents="6" NumberOfTuples="27" format="binary" RangeMin="0.0121503782802162" RangeMax="0.0121503782802162">
+ AQAAAACAAAAQBQAAMAAAAA==eJxTOHNcy+dRx36H62928vZ+t9ynzxnmbfDAkgEHUBhVP6p+VP2o+mGqHgCntDx4
+ <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+ <Value index="0">
+ 0.01215037828
+ </Value>
+ <Value index="1">
+ 0.01215037828
+ </Value>
+ </InformationKey>
+ </DataArray>
+ <DataArray type="Float64" Name="sigma_total_ip" NumberOfComponents="6" NumberOfTuples="27" format="binary" RangeMin="3349098.003711932" RangeMax="3349098.003711932">
+ AQAAAACAAAAQBQAAKAAAAA==eJzzsfn9/7yQ88G+ZYkxk7gt4DQDDuAzqn5U/aj6UfXDVD0ANBM1Zw==
+ <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+ <Value index="0">
+ 3349098.0037
+ </Value>
+ <Value index="1">
+ 3349098.0037
+ </Value>
+ </InformationKey>
+ </DataArray>
+ <DataArray type="Float64" Name="saturation_ip" NumberOfTuples="27" format="binary" RangeMin="0.305951624766487" RangeMax="0.305951624766487">
+ AQAAAACAAADYAAAAFAAAAA==eJyb/Hah/LYpl+0nDzMaAOMDfHU=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_e_ip" NumberOfTuples="27" format="binary" RangeMin="0.877053965259221" RangeMax="0.877053965259221">
+ AQAAAACAAADYAAAAFAAAAA==eJz7vtG46rLAG/vvw4wGAGvgdnI=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_em_ip" NumberOfTuples="27" format="binary" RangeMin="0.263419138814884" RangeMax="0.263419138814884">
+ AQAAAACAAADYAAAAFAAAAA==eJxTyp326fbtC/ZKw4wGAHEYgzU=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_eM_ip" NumberOfTuples="27" format="binary" RangeMin="0.485693787277066" RangeMax="0.485693787277066">
+ AQAAAACAAADYAAAAFAAAAA==eJybl8OXOlv0vv28YUYDALKOWOo=
+ </DataArray>
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diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_160_t_2.000000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_160_t_2.000000.vtu
new file mode 100644
index 00000000000..bc4f43979c6
--- /dev/null
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diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_200_t_2.500000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_200_t_2.500000.vtu
new file mode 100644
index 00000000000..c49959d4fec
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diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_240_t_3.000000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_240_t_3.000000.vtu
new file mode 100644
index 00000000000..47d50bc04d6
--- /dev/null
+++ b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_240_t_3.000000.vtu
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new file mode 100644
index 00000000000..8f56ebb6685
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new file mode 100644
index 00000000000..d6ea247bcdf
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diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_360_t_4.500000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_360_t_4.500000.vtu
new file mode 100644
index 00000000000..88299be904a
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diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_440_t_5.500000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_440_t_5.500000.vtu
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diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_480_t_6.000000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_480_t_6.000000.vtu
new file mode 100644
index 00000000000..b7b0a970324
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+ <DataArray type="Float64" Name="material_state_variable_em_ip" NumberOfTuples="27" format="binary" RangeMin="0.262610072732056" RangeMax="0.262610072732056">
+ AQAAAACAAADYAAAAFAAAAA==eJw7+b+uata5C/YnhxkNAOItjM4=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_eM_ip" NumberOfTuples="27" format="binary" RangeMin="0.426186843691185" RangeMax="0.426186843691185">
+ AQAAAACAAADYAAAAFAAAAA==eJwTev5Cb6nbbXuhYUYDALRQbh0=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_SrM_ip" NumberOfTuples="27" format="binary" RangeMin="0.0095382271205745" RangeMax="0.0095382271205745">
+ AQAAAACAAADYAAAAEwAAAA==eJyzbY3WOd7RbG87zGgATfhafw==
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_a_scan_ip" NumberOfTuples="27" format="binary" RangeMin="0" RangeMax="0">
+ AQAAAACAAADYAAAADAAAAA==eJxjYBieAAAA2AAB
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_re_ip" NumberOfTuples="27" format="binary" RangeMin="0.917065133616692" RangeMax="0.917065133616692">
+ AQAAAACAAADYAAAAFAAAAA==eJxT+LD014yIt/YKw4wGAOO1gWo=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[0]_ip" NumberOfTuples="27" format="binary" RangeMin="1920" RangeMax="1920">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBeQ4Mw4wGAKyDF2s=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[1]_ip" NumberOfTuples="27" format="binary" RangeMin="480" RangeMax="480">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBOgeGYUYDAEa0FAs=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[2]_ip" NumberOfTuples="27" format="binary" RangeMin="1" RangeMax="1">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBD/YMw4wGADZoH/Y=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[3]_ip" NumberOfTuples="27" format="binary" RangeMin="1" RangeMax="1">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBD/YMw4wGADZoH/Y=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_stored energy_ip" NumberOfTuples="27" format="binary" RangeMin="0" RangeMax="0">
+ AQAAAACAAADYAAAADAAAAA==eJxjYBieAAAA2AAB
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_disspated energy_ip" NumberOfTuples="27" format="binary" RangeMin="0" RangeMax="0">
+ AQAAAACAAADYAAAADAAAAA==eJxjYBieAAAA2AAB
+ </DataArray>
+ </FieldData>
+ <Piece NumberOfPoints="8" NumberOfCells="1">
+ <PointData Scalars="pressure">
+ <DataArray type="Float64" Name="pressure" format="binary" RangeMin="-110000000" RangeMax="-110000000">
+ AQAAAACAAABAAAAAEwAAAA==eJxjYGBguGc56yADmTQAVN4TkQ==
+ </DataArray>
+ </PointData>
+ <CellData>
+ </CellData>
+ <Points>
+ <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="1.7320508075688772">
+ AQAAAACAAADAAAAAHAAAAA==eJxjYMAHPtjjlcaQh/GJ1YdLPy51mDQAp2EONQ==
+ <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+ <Value index="0">
+ 0
+ </Value>
+ <Value index="1">
+ 1.7320508076
+ </Value>
+ </InformationKey>
+ </DataArray>
+ </Points>
+ <Cells>
+ <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="7">
+ AQAAAACAAABAAAAAHgAAAA==eJxjYIAARijNDKWZoDQLlGaF0uxQmg1KAwAC8AAd
+ </DataArray>
+ <DataArray type="Int64" Name="offsets" format="binary" RangeMin="8" RangeMax="8">
+ AQAAAACAAAAIAAAACwAAAA==eJzjYIAAAABIAAk=
+ </DataArray>
+ <DataArray type="UInt8" Name="types" format="binary" RangeMin="12" RangeMax="12">
+ AQAAAACAAAABAAAACQAAAA==eJzjAQAADQAN
+ </DataArray>
+ </Cells>
+ </Piece>
+ </UnstructuredGrid>
+</VTKFile>
diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_80_t_1.000000.vtu b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_80_t_1.000000.vtu
new file mode 100644
index 00000000000..897917704da
--- /dev/null
+++ b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/confined_compression_ts_80_t_1.000000.vtu
@@ -0,0 +1,101 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+ <UnstructuredGrid>
+ <FieldData>
+ <DataArray type="Float64" Name="epsilon_ip" NumberOfComponents="6" NumberOfTuples="27" format="binary" RangeMin="0.0075243833521511" RangeMax="0.0075243833521511">
+ AQAAAACAAAAQBQAAMAAAAA==eJwr7dnh9vhi3f5738IMPf0kd3Wo/GPsWclixYADlI6qH1U/qn5U/TBVDwDA2D9R
+ <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+ <Value index="0">
+ 0.0075243833522
+ </Value>
+ <Value index="1">
+ 0.0075243833522
+ </Value>
+ </InformationKey>
+ </DataArray>
+ <DataArray type="Float64" Name="sigma_total_ip" NumberOfComponents="6" NumberOfTuples="27" format="binary" RangeMin="3338396.501585605" RangeMax="3338396.501585605">
+ AQAAAACAAAAQBQAAKAAAAA==eJzLqVm2yuus40EFtfmlRw5ZwmkGHCBnVP2o+lH1o+qHqXoAQ5tElw==
+ <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+ <Value index="0">
+ 3338396.5016
+ </Value>
+ <Value index="1">
+ 3338396.5016
+ </Value>
+ </InformationKey>
+ </DataArray>
+ <DataArray type="Float64" Name="saturation_ip" NumberOfTuples="27" format="binary" RangeMin="0.302913451504564" RangeMax="0.302913451504564">
+ AQAAAACAAADYAAAAFAAAAA==eJx7evCd5Puky/ZPhxkNADY7iLE=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_e_ip" NumberOfTuples="27" format="binary" RangeMin="0.885757322639388" RangeMax="0.885757322639388">
+ AQAAAACAAADYAAAAFAAAAA==eJy7sX3uXvmIN/Y3hhkNAD5Feqo=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_em_ip" NumberOfTuples="27" format="binary" RangeMin="0.263413933063356" RangeMax="0.263413933063356">
+ AQAAAACAAADYAAAAFAAAAA==eJybHf5F5tjtC/azhxkNALvqfsc=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_eM_ip" NumberOfTuples="27" format="binary" RangeMin="0.492588670523552" RangeMax="0.492588670523552">
+ AQAAAACAAADYAAAAFAAAAA==eJwrvj5x4aS2+/bFw4wGANJ8fsc=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_SrM_ip" NumberOfTuples="27" format="binary" RangeMin="0.0078636049826494" RangeMax="0.0078636049826494">
+ AQAAAACAAADYAAAAEwAAAA==eJzz97hqeFqqwd5/mNEAS+9X3A==
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_a_scan_ip" NumberOfTuples="27" format="binary" RangeMin="0" RangeMax="0">
+ AQAAAACAAADYAAAADAAAAA==eJxjYBieAAAA2AAB
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_re_ip" NumberOfTuples="27" format="binary" RangeMin="0.975596147171787" RangeMax="0.975596147171787">
+ AQAAAACAAADYAAAAEwAAAA==eJzjn+2WKWrx3p5/mNEAPn1MXQ==
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[0]_ip" NumberOfTuples="27" format="binary" RangeMin="320" RangeMax="320">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBEgeGYUYDANbZEv0=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[1]_ip" NumberOfTuples="27" format="binary" RangeMin="80" RangeMax="80">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBEAeGYUYDAHEKD50=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[2]_ip" NumberOfTuples="27" format="binary" RangeMin="1" RangeMax="1">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBD/YMw4wGADZoH/Y=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_RungeKutta_InternalStateVariables[3]_ip" NumberOfTuples="27" format="binary" RangeMin="1" RangeMax="1">
+ AQAAAACAAADYAAAAEQAAAA==eJxjYACBD/YMw4wGADZoH/Y=
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_stored energy_ip" NumberOfTuples="27" format="binary" RangeMin="0" RangeMax="0">
+ AQAAAACAAADYAAAADAAAAA==eJxjYBieAAAA2AAB
+ </DataArray>
+ <DataArray type="Float64" Name="material_state_variable_disspated energy_ip" NumberOfTuples="27" format="binary" RangeMin="0" RangeMax="0">
+ AQAAAACAAADYAAAADAAAAA==eJxjYBieAAAA2AAB
+ </DataArray>
+ </FieldData>
+ <Piece NumberOfPoints="8" NumberOfCells="1">
+ <PointData Scalars="pressure">
+ <DataArray type="Float64" Name="pressure" format="binary" RangeMin="-110000000" RangeMax="-110000000">
+ AQAAAACAAABAAAAAEwAAAA==eJxjYGBguGc56yADmTQAVN4TkQ==
+ </DataArray>
+ </PointData>
+ <CellData>
+ </CellData>
+ <Points>
+ <DataArray type="Float64" Name="Points" NumberOfComponents="3" format="binary" RangeMin="0" RangeMax="1.7320508075688772">
+ AQAAAACAAADAAAAAHAAAAA==eJxjYMAHPtjjlcaQh/GJ1YdLPy51mDQAp2EONQ==
+ <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+ <Value index="0">
+ 0
+ </Value>
+ <Value index="1">
+ 1.7320508076
+ </Value>
+ </InformationKey>
+ </DataArray>
+ </Points>
+ <Cells>
+ <DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="7">
+ AQAAAACAAABAAAAAHgAAAA==eJxjYIAARijNDKWZoDQLlGaF0uxQmg1KAwAC8AAd
+ </DataArray>
+ <DataArray type="Int64" Name="offsets" format="binary" RangeMin="8" RangeMax="8">
+ AQAAAACAAAAIAAAACwAAAA==eJzjYIAAAABIAAk=
+ </DataArray>
+ <DataArray type="UInt8" Name="types" format="binary" RangeMin="12" RangeMax="12">
+ AQAAAACAAAABAAAACQAAAA==eJzjAQAADQAN
+ </DataArray>
+ </Cells>
+ </Piece>
+ </UnstructuredGrid>
+</VTKFile>
diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/generate-reference-solution.py b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/generate-reference-solution.py
new file mode 100755
index 00000000000..0637b20f49f
--- /dev/null
+++ b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/generate-reference-solution.py
@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+# invoke with
+# LD_LIBRARY_PATH="<OGS_BUILD_DIR>/lib:$LD_LIBRARY_PATH" ./generate-reference-solution.py
+
+
+from pathlib import Path
+
+import mtest
+import numpy as np
+import tfel.tests # noqa: F401 necessary for Boost.Python type converters
+from ogs_and_mfront import (
+ aggregate_ogs_results,
+ generate_reference_meshes,
+ plot,
+ read_mtest_results,
+ read_single_element_ogs_results,
+ report_and_plot_summary,
+ to_dataframes_with_mfront_names,
+ write_test_definition_snippet,
+)
+
+if not Path("out").exists():
+ Path("out").mkdir()
+ with Path("out/.gitignore").open("w") as fh:
+ fh.write("*\n")
+
+if not Path("out/plot_mtest").exists():
+ Path("out/plot_mtest").mkdir()
+
+if not Path("out/plot_mtest_vs_ogs").exists():
+ Path("out/plot_mtest_vs_ogs").mkdir()
+
+dt = 0.0125
+mtest_output_file = "out/confined_compression_mtest.res"
+ogs_output_file = "out/ogs/confined_compression.pvd" # OGS must be run manually, e.g., run ctest and link ctest output dir
+mesh_filename = "meshes/cube_1e0_1x1x1_hex8.vtu"
+
+check_times = np.arange(0.5, 6 + 0.5 / 2, 0.5)
+
+ref_mesh_filename_template = "confined_compression_ts_{ts}_t_{t:.6f}.vtu"
+
+
+def exec_mtest():
+ m = mtest.MTest()
+ m.setBehaviour(
+ "generic",
+ "libOgsMFrontBehaviourBentoniteGeneralModForCTestsOnly",
+ "BentoniteBehaviour",
+ )
+ m.setScalarInternalStateVariableInitialValue("e", 0.9)
+ m.setScalarInternalStateVariableInitialValue("em", 0)
+ m.setScalarInternalStateVariableInitialValue("eM", 0)
+ m.setScalarInternalStateVariableInitialValue("SrM", 0)
+ m.setScalarInternalStateVariableInitialValue("a_scan", 0)
+ m.setScalarInternalStateVariableInitialValue("re", 0)
+
+ # initial value of the gradients (strain+suction)
+ m.setGradientsInitialValues([0, 0, 0, 0, 0, 0, -110e6])
+ # initial values of the thermodynamic forces (total stress+Saturation)
+ m.setThermodynamicForcesInitialValues([-2e6, -2e6, -2e6, 0, 0, 0, 0.345])
+
+ m.setImposedThermodynamicForce("StressXX", {0: -2e6, 6: -4e6})
+ # m.setImposedGradient('StrainXX', 0)
+ m.setImposedGradient("StrainYY", 0)
+ m.setImposedGradient("StrainZZ", 0)
+ m.setImposedGradient("StrainXY", 0)
+ m.setImposedGradient("StrainXZ", 0)
+ m.setImposedGradient("StrainYZ", 0)
+ m.setImposedGradient("LiquidPressure", -110e6)
+ #
+ m.setExternalStateVariable("AirPressure", 0)
+ m.setExternalStateVariable("Temperature", 273.15)
+
+ # output file
+ m.setOutputFileName(mtest_output_file)
+ m.setOutputFilePrecision(15)
+
+ # // Imposing the time
+ time = np.arange(
+ 0, 6 + dt / 2, dt
+ ).tolist() # conversion to list necessary to satisfy mtest Python bindings
+ m.setTimes(time)
+
+ print("## Executing MTest...")
+ m.execute()
+
+
+exec_mtest()
+
+df_ref = read_mtest_results(mtest_output_file)
+
+report_and_plot_summary(df_ref, file_prefix="out/plot_mtest/")
+
+generate_reference_meshes(
+ mesh_filename, df_ref, check_times, ref_mesh_filename_template
+)
+
+ts_ogs, recs_ogs = read_single_element_ogs_results(ogs_output_file)
+
+recs_ogs_agg = aggregate_ogs_results(recs_ogs)
+
+dfs_ogs_agg_mfront = to_dataframes_with_mfront_names(recs_ogs_agg, ts_ogs)
+
+print("\n## Plotting comparison between OGS and MTest...")
+plot(
+ df_ref,
+ dfs_ogs_agg_mfront["min"],
+ dfs_ogs_agg_mfront["max"],
+ labels=["mtest", "ogs min", "ogs max"],
+ file_prefix="out/plot_mtest_vs_ogs/",
+ quantities="intersection",
+)
+
+write_test_definition_snippet(
+ df_ref.columns.values,
+ dfs_ogs_agg_mfront["min"].columns.values,
+ "confined_compression",
+ "out/test_definition.xml",
+)
diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/meshes b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/meshes
new file mode 120000
index 00000000000..a0acdbe4c66
--- /dev/null
+++ b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/meshes
@@ -0,0 +1 @@
+../meshes/
\ No newline at end of file
diff --git a/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/ogs_and_mfront.py b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/ogs_and_mfront.py
new file mode 100644
index 00000000000..8eccfed3eda
--- /dev/null
+++ b/Tests/Data/ThermoRichardsMechanics/MFront/BentoniteBehaviourGeneralMod/0d_confined_compression/ogs_and_mfront.py
@@ -0,0 +1,376 @@
+import contextlib
+import re
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+import pyvista as pv
+
+# ATM only for symmetric tensors. TODO extend
+map_tensor_component_name_to_ogs_index = {
+ "XX": 0,
+ "YY": 1,
+ "ZZ": 2,
+ "XY": 3,
+ "YZ": 4,
+ "XZ": 5,
+}
+
+map_ogs_index_to_component_name = {
+ 3: {0: "X", 1: "Y", 2: "Z"},
+ 6: {index: name for name, index in map_tensor_component_name_to_ogs_index.items()},
+ 9: {index: "XYZ"[index // 3] + "XYZ"[index % 3] for index in range(9)},
+}
+
+
+map_mfront_name_to_ogs = {
+ "Strain": "epsilon_ip",
+ "Stress": "sigma_total_ip",
+ "LiquidPressure": "pressure",
+ "Saturation": "saturation_ip",
+}
+
+map_ogs_name_to_mfront = {ogs: mfront for mfront, ogs in map_mfront_name_to_ogs.items()}
+
+
+def parse_mtest_res_header(f):
+ multi_comp_re = re.compile(r"([0-9]+)th component of the (.*) [(](.*)[)]")
+
+ names = []
+ with Path(f).open() as fh:
+ for line in fh:
+ if not line.startswith("#"):
+ break
+ col, name = line.strip().split(": ")
+
+ if m := multi_comp_re.match(name):
+ name = f"{m.group(3)}"
+ names.append(name)
+ return names
+
+
+def read_mtest_results(mtest_output_file):
+ names = parse_mtest_res_header(mtest_output_file)
+ df_mtest = pd.read_csv(
+ mtest_output_file, sep=" ", comment="#", header=None, names=names, dtype=float
+ )
+ df_mtest.index = df_mtest.index.rename("time_step")
+ return df_mtest
+
+
+def read_single_element_ogs_results(pvd_file):
+ reader = pv.get_reader(pvd_file)
+
+ recs = []
+ ts = reader.time_values
+
+ for ti, _t in enumerate(ts):
+ reader.set_active_time_point(ti)
+ mesh = reader.read()[0]
+ assert mesh.n_cells == 1
+ if ti == 0:
+ N = mesh.n_points
+ else:
+ assert mesh.n_points == N
+
+ rec = dict(mesh.point_data)
+ assert set(rec.keys()).isdisjoint(mesh.cell_data.keys())
+ rec.update(mesh.cell_data)
+ assert set(rec.keys()).isdisjoint(mesh.field_data.keys())
+ rec.update(mesh.field_data)
+
+ recs.append(rec)
+
+ assert len(recs) != 0
+
+ shapes = {field: value.shape for field, value in recs[0].items()}
+
+ # assert same number of components and tuples for all timesteps
+ for rec in recs[1:]:
+ for field, value in rec.items():
+ assert value.shape == shapes[field]
+
+ return ts, recs
+
+
+def aggregate(rec, f):
+ return {k: f(v, axis=0) for k, v in rec.items()}
+
+
+def aggregate_ogs_results(recs):
+ names = ("min", "max", "mean", "std")
+ fs = (np.min, np.max, np.mean, np.std)
+
+ return {n: [aggregate(rec, f) for rec in recs] for n, f in zip(names, fs)}
+ # recs_min = [ aggregate(rec, np.min) for rec in recs ]
+ # print(recs_min)
+
+
+def to_dataframes_with_mfront_names(recs_ogs_agg, ts_ogs):
+ # suffix _mfront denotes MFront column naming scheme
+ recs_ogs_agg_mfront = {
+ agg: ogs_names_to_mfront(recs) for agg, recs in recs_ogs_agg.items()
+ }
+ dfs_ogs_agg_mfront = {
+ agg: pd.DataFrame.from_records(recs, index=pd.Index(ts_ogs, name="time"))
+ for agg, recs in recs_ogs_agg_mfront.items()
+ }
+ for df in dfs_ogs_agg_mfront.values():
+ df["time"] = ts_ogs
+
+ return dfs_ogs_agg_mfront
+
+
+def ogs_names_to_mfront(recs_ogs):
+ def gen_mfront_keys_values(rec_ogs):
+ for field_ogs, v in rec_ogs.items():
+ for comp_idx, comp_value in enumerate(np.atleast_1d(v)):
+ # print(ogs_name_to_mfront(field_ogs, comp_idx, np.size(v)), comp_value)
+ yield ogs_name_to_mfront(field_ogs, comp_idx, np.size(v)), comp_value
+
+ recs_mfront = []
+ for rec in recs_ogs:
+ recs_mfront.append(dict(gen_mfront_keys_values(rec)))
+
+ return recs_mfront
+
+
+def report_and_plot_summary(df_res, file_prefix):
+ df_agg = df_res.agg(["min", "max"])
+ rec_max = df_agg.loc["max"]
+
+ ser_range = (rec_max - df_agg.loc["min"]).drop("time")
+
+ print(
+ "\n## The following quantities did not change over the course of the simulation:"
+ )
+ for qty in ser_range[ser_range == 0].index.array:
+ print(f" {qty} (constant = {rec_max[qty]:g})")
+
+ print("\n## Changing quantities are plotted...")
+ changing_quantities = ser_range[ser_range != 0].index.array
+
+ plot(df_res, quantities=changing_quantities, file_prefix=file_prefix)
+
+
+def common_columns(*dfs):
+ if not dfs:
+ return set()
+
+ return set(dfs[0].columns.to_numpy()).intersection(
+ *(df.columns.to_numpy() for df in dfs[1:])
+ )
+
+
+def plot(
+ *dfs, labels=None, quantities="union", file_prefix="", file_suffix="", diff=None
+):
+ assert len(dfs) >= 1
+
+ if isinstance(quantities, str):
+ if quantities == "intersection":
+ quantities = common_columns(*dfs)
+ elif quantities == "union":
+ quantities = set(dfs[0].columns.to_numpy()).union(
+ *(df.columns.to_numpy() for df in dfs[1:])
+ )
+ else:
+ msg = f"Unknown magic value for quantities argument: '{quantities}'"
+ raise ValueError(msg)
+
+ if diff is None:
+ diff = len(dfs) > 1
+
+ for qty in sorted(quantities):
+ if qty == "time":
+ continue
+
+ if diff:
+ fig, (ax, ax_diff) = plt.subplots(2, sharex=True)
+ ax_last = ax_diff
+ ax_diff.set_ylabel("absolute difference")
+
+ else:
+ fig, ax = plt.subplots()
+ ax_last = ax
+ # ax.set_ylabel(qty)
+
+ for i, df in enumerate(dfs):
+ assert "time" in df.columns
+ try:
+ kwargs = {}
+ try:
+ kwargs["label"] = labels[i]
+ except TypeError:
+ if len(dfs) > 1:
+ kwargs["label"] = f"df #{i}"
+
+ df.plot("time", qty, ax=ax, **kwargs)
+ except KeyError as e:
+ print(f"KeyError in dfs[{i}]:", e)
+
+ if diff:
+ ax_diff.plot([], []) # plot nothing to skip first plot style
+ df_ref = dfs[0]
+ ax_abs_max_095 = 0
+ ax_abs_max = 0
+ some_below_0 = False
+ some_above_0 = False
+
+ for i, df in enumerate(dfs[1:]):
+ ts = df["time"].to_numpy()
+ try:
+ assert np.allclose(
+ ts, df_ref["time"].to_numpy(), atol=1e-13, rtol=0
+ )
+ except AssertionError:
+ print(ts - df_ref["time"].to_numpy())
+ raise
+
+ kwargs = {}
+ with contextlib.suppress(TypeError):
+ kwargs["label"] = f"{labels[i+1]} $-$ {labels[0]}"
+
+ ds = df[qty].to_numpy() - df_ref[qty].to_numpy()
+
+ ax_diff.plot(ts, ds, **kwargs)
+
+ ds_abs = np.abs(ds)
+ ax_abs_max_095 = max(ax_abs_max_095, np.quantile(ds_abs, 0.95))
+ ax_abs_max = max(ax_abs_max, np.max(ds_abs))
+ some_below_0 = some_below_0 or np.any(ds < 0)
+ some_above_0 = some_above_0 or np.any(ds > 0)
+
+ ax_diff.legend()
+ if ax_abs_max != 0:
+ if ax_abs_max_095 != 0:
+ linthresh = ax_abs_max_095
+ else:
+ linthresh = 1e-15 * ax_abs_max
+
+ ax_diff.set_yscale("symlog", linthresh=linthresh)
+ if some_above_0:
+ ax_diff.axhline(linthresh, ls=":", color="gray")
+ if some_below_0:
+ ax_diff.axhline(-linthresh, ls=":", color="gray")
+ else:
+ ax_diff.annotate(
+ "all differences are zero", (0.05, 0.05), xycoords="axes fraction"
+ )
+ ax_diff.axhline(0, ls=":", color="gray")
+
+ ax.set_title(qty)
+ ax_last.set_xlabel("$t$ / s")
+ fig = ax.get_figure()
+ print(f" {file_prefix}{qty}{file_suffix}.png")
+ fig.savefig(f"{file_prefix}{qty}{file_suffix}.png")
+ plt.close(fig)
+
+
+def mfront_to_ogs(rec):
+ ogs_rec = {}
+
+ for k, v in rec.items():
+ if k == "time_step":
+ continue
+
+ name, comp = mfront_name_to_ogs(k)
+
+ if comp is None:
+ ogs_rec[name] = np.array([v])
+ elif name not in ogs_rec:
+ ogs_rec[name] = np.array([0] * (comp - 1) + [v])
+ else:
+ arr = ogs_rec[name]
+ if len(arr) <= comp:
+ arr.resize(comp + 1, refcheck=False)
+ arr[comp] = v
+
+ return ogs_rec
+
+
+def mfront_name_to_ogs(k):
+ assert k != "time"
+ if k[-2:] in map_tensor_component_name_to_ogs_index:
+ name = k[:-2]
+ comp = map_tensor_component_name_to_ogs_index[k[-2:]]
+ else:
+ name = k
+ comp = None
+
+ if name in map_mfront_name_to_ogs:
+ name = map_mfront_name_to_ogs[name]
+ else:
+ name = f"material_state_variable_{name}_ip"
+
+ return name, comp
+
+
+def ogs_name_to_mfront(name, comp, num_comps):
+ if name.startswith("material_state_variable_") and name.endswith("_ip"):
+ assert num_comps == 1 # other cases not yet implemented
+ return name[len("material_state_variable_") : -len("_ip")]
+
+ if num_comps == 1:
+ comp_suffix = ""
+ else:
+ comp_suffix = map_ogs_index_to_component_name[num_comps][comp]
+
+ name_mfront = map_ogs_name_to_mfront.get(name, name)
+
+ return name_mfront + comp_suffix
+
+
+def generate_reference_meshes(
+ input_mesh, df_res_mtest, time_steps, filename_template, num_int_pts
+):
+ mesh_ic = pv.read(input_mesh)
+ mesh_ic.point_data.clear()
+ mesh_ic.cell_data.clear()
+ mesh_ic.field_data.clear()
+ N = mesh_ic.n_points
+
+ df_res_t = df_res_mtest.copy(deep=False)
+ df_res_t["time_step"] = df_res_t.index
+ df_res_t = df_res_t.set_index("time")
+
+ for t in time_steps:
+ mesh = mesh_ic.copy(deep=False)
+ rec = df_res_t.loc[t]
+ for k, v in mfront_to_ogs(rec).items():
+ if k.endswith("_ip"):
+ mesh.field_data[k] = np.tile(v, (num_int_pts, 1))
+ else:
+ mesh.point_data[k] = np.tile(v, (N, 1))
+
+ mesh.save(filename_template.format(t=t, ts=int(rec["time_step"])))
+
+
+def write_test_definition_snippet(
+ fields_mfront, fields_ogs_mfront, regex_prefix, output_file
+):
+ fields1 = {
+ mfront_name_to_ogs(field)[0] for field in fields_mfront if field != "time"
+ }
+ fields2 = {
+ mfront_name_to_ogs(field)[0] for field in fields_ogs_mfront if field != "time"
+ }
+
+ fields_ogs = fields1 & fields2
+
+ with Path(output_file).open("w") as fh:
+ fh.write(" <test_definition>")
+
+ for field in sorted(fields_ogs):
+ fh.write(
+ f"""
+ <vtkdiff>
+ <regex>{regex_prefix}_ts_.*_t_.*[.]vtu</regex>
+ <field>{field}</field>
+ <absolute_tolerance>0.0</absolute_tolerance>
+ <relative_tolerance>0.0</relative_tolerance>
+ </vtkdiff>"""
+ )
+
+ fh.write("\n </test_definition>\n")
--
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